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iqbal-lab / eval_wgs_for_public_health

Datasets, truthsets, auto-analysis for evaluating WGS pipelines for public health needs. Starting with TB
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Separation of overview and results #1

Closed iqbal-lab closed 8 years ago

iqbal-lab commented 8 years ago

Can we split things out please so readme has a list of what tests we are running, and then one markdown report for each test, with results?

iqbal-lab commented 8 years ago

Naming:

  1. Spiking tests (using spiked reference genome to measure false negative rates for SNPs)
  2. Cluster detection from real outbreak
  3. Species identification
  4. Full-spectrum mutation analysis with F11 reference genome
  5. Resistance prediction compared with HAIN and phenotype
iqbal-lab commented 8 years ago

We should probably add:

  1. Contamination measurement and general QC
iqbal-lab commented 8 years ago

Done